def test_validate_config_nopipelines(self):
input_data = """
{"number_of_example_samples": 1,
"pipeline": "catsup-kraken2",
"upload":
{
"s3":
{
"bucket": "s3://mmm-sp3-alpha",
"s3cmd-config": "/tmp/catsup/.s3cfg-catsup"
}}}
"""
input_dict = json.loads(input_data)
expected_results = False
result = validate.validate_config(input_dict)
self.assertEqual(expected_results, result)
def read_cfg(cfg_file, cfg_file_example):
if not pathlib.Path(cfg_file).exists():
if pathlib.Path(cfg_file_example).exists():
print(f"{cfg_file} not found. Copying from {cfg_file_example}")
shutil.copyfile(cfg_file_example, cfg_file)
print(
f"Please edit {cfg_file} to make it work with your environment"
)
sys.exit(0)
else:
logging.error(
f"Couldn't find config file ({cfg_file}) or config file example ({cfg_file_example})"
)
sys.exit(1)
global cfg
with open(cfg_file) as f:
cfg = json.loads(f.read())
if not validate.validate_config(cfg):
logging.error(f"Config file ({cfg_file}) is not valid.")
sys.exit(1)
def test_validate_config_fullconfig(self):
input_data = """
{"number_of_example_samples": 1,
"pipeline": "catsup-kraken2",
"pipelines": {
"catsup-kraken2":
{
"script": "/tmp/catsup/catsup-kraken2.nf",
"image": "/tmp/catsup/fatos.img",
"human_ref": "/tmp/catsup/human_ref"
}},
"upload":
{
"s3":
{
"bucket": "s3://mmm-sp3-alpha",
"s3cmd-config": "/tmp/catsup/.s3cfg-catsup"
}}}
"""
input_dict = json.loads(input_data)
expected_results = True
result = validate.validate_config(input_dict)
self.assertEqual(expected_results, result)
def test_validate_config_noconfig(self):
input_data = '{}'
expected_results = False
result = validate.validate_config(input_data)
self.assertEqual(expected_results, result)